Culture-independent analysis of the microbial composition of the African traditional fermented foods poto poto and degue by using three different DNA extraction methods

The microbial composition of the traditional fermented foods poto poto (a maize dough from the Rep. of Congo) and degue (a millet dough from Burkina Faso) was studied by a culture-independent approach using TTGE to separate the amplified target V3 region of the 16S rRNA gene from total microbial community, followed by DNA sequencing and homology search. Three different extraction methods were used. Guanidium thiocyanate-based DNA extraction provided better performance regarding purity and DNA yield, allowing the detection of a higher number of DNA bands by TTGE in poto poto. By contrast, all three methods yielded similar results for degue samples, indicating that the performance of the DNA extraction method largely depends on the food composition. Sequencing of DNA bands from TTGE gels corresponding to poto poto samples revealed the presence of Lactobacillus gasseri, Enterococcus sp., Escherichia coli, Lactobacillus plantarum/paraplantarum, Lactobacillus acidophilus, Lactobacillus delbrueckii, Bacillus sp., Lactobacillus reuteri and Lactobacillus casei. The following bacteria were identified in degue: L. gasseri, Enterococcus sp., E. coli, Lactobacillus fermentum, Lactobacillus brevis, and L. casei. (c) 2006 Elsevier B.V All rights reserved.